We present a comparative study of proton dissociation in various functional acidic units that are promising candidates as building blocks for polymeric electrolyte membranes. Minimum energy structures for four acidic moieties with clusters of 1-6 water molecules were determined using density functional theory at the B3LYP/6-311G** level starting from chemically rational initial configurations. The perfluoro sulfonyl imide acid group (CF(3)CF(2)SO(2)NHSO(2)CF(3)) was observed to be the strongest acid, due to the substantial electron withdrawing effect of both fluorocarbon groups. The hydrophilic functional group (CH(3)OC(6)H(3)OCH(3)C(6)H(4)SO(3)H) of sulfonated polyetherether ketone (SPEEK) membrane was found to be the strongest base, with the acidic proton dissociation requiring the addition of six water molecules and the hydrated proton being more tightly bound to the conjugate base. Even though both perfluoro sulfonyl imides and sulfonic acids (hydrophilic functional groups for sulfonyl imide and Nafion ionomers, respectively) required only three water molecules to exhibit spontaneous proton dissociation, the largest possible solvent-separated hydronium ion was attained only for the sulfonyl imide moiety. These results provide a rationale for the enhanced conductivity of perfluorinated sulfonyl imide-based membranes relative to that of the widely used Nafion membrane.